Comparative gene-centric metagenomics of the rumen microbiome

The complex microbiome of the rumen functions as an exceptionally effective system for the conversion of plant cell wall biomass to microbial protein, short chain fatty acids, and gases including hydrogen and methane. As such, it provides a unique genetic resource for plant cell wall degrading microbial enzymes that could be used in the production of biofuels from lignocellulose. Since a majority of this complex microbiome has yet to be fully cultivated and explored, uncharacterized microbial populations may alter their physiological profile and possess critical enzymatic components essential for the breakdown of fiber-based feeds. The objectives of this research were to provide information pertaining to the physiological ecology of both of the rumen community and of specialist fiber-degraders. We proposed to use culture-independent metagenomic approaches that addressed the differences in the rumen microbial community and, more importantly, described and linked their metabolic potential. Our hypothesis was that the most important organisms and their gene sets involved in the most efficient hydrolysis of plant cell walls are associated with the fiber portion of the rumen digesta. Therefore, we used a cadre of metagenomic approaches to analyze the phylogenetic and genomic content of the fiber-associated rumen communities. This approach allowed us to not only identify the fiber-associated microbial community at great phylogenetic depth but also multiple functional gene sets responsible for efficient fiber degradation. Additionally, we were able to identify one specific gene cluster that may be an indicator of intra-species diversity within fiber-degrading specialists.